The advent of DNA microarray technology makes it possible to build an array of hundreds of thousands of DNA sequences in a very small area, such as the size of a microscopic slide. See, e.g., U.S. Pat. No. 6,375,903 and U.S. Pat. No. 5,143,854, each of which is hereby incorporated by reference in its entirety. The disclosure of U.S. Pat. No. 6,375,903 enables the construction of so-called maskless array synthesizer (MAS) instruments in which light is used to direct synthesis of the DNA sequences, the light direction being performed using a digital micromirror device (DMD), also known as a digital light processor (DLP). Using an MAS instrument, the selection of DNA sequences to be constructed in the microarray is under software control so that individually customized arrays can be built to order. In general, MAS based DNA microarray synthesis technology allows for the parallel synthesis of over 800,000 unique oligonucleotides in a very small area of on a standard microscope slide. The microarrays are generally synthesized by using light to direct which oligonucleotides are synthesized at specific locations on an array, these locations being called features. Typically, one nucleotide sequence is synthesized at each feature of the array, i.e. there are multiple probes in each feature, but all those probes have the same nucleotide sequence. For certain applications it would be advantageous to have oligonucleotides of different sequences present within one feature of the array, and be able to control the ratio and direction (5′-3′, or 3′-5′) of these oligonucleotides.
One use of microarrays is to perform sequence analysis of DNA isolated from living organisms. Science has now made available generalized DNA sequences of the entire genomes of several important organisms, including humans. One technique that can be used to identify a genetic variant is to sequence the genomic DNA of an individual and then to compare that sequence to the reference sequence of that organism. It has been found that many differences in DNA sequence are presented as single variations in DNA sequence, often referred to as single nucleotide polymorphisms or SNPs. By performing a sequence comparison between the entire sequenced genome of an individual and the reference genome of that species, it is by this brute force mechanism to identify the SNPs for that individual. However, this process is too laborious to be practical for SNP detection on a large scale. The identification and analysis of SNPs is therefore a technology to which much attention has been devoted.